Andujar had beaten Mayer in the round of 16 in last year's Bucharest event on his way to the final, but the German used a run of nine consecutive games to win Sunday.
Andujar was leading 3-2 in the first set before Mayer rallied to win the next four. The second-seeded German then stormed out to a 5-0 lead in the second set, and after Andujar managed a hold, Mayer served out for the match.
Mayer, ranked 24th, had been 0-4 in ATP finals, including a loss to Nikolay Davydenko in the Munich final back in May. He earned $93,000 for the victory.
Andujar, seeded fourth, was appearing in his third final of the season. He beat Potito Starace for his first career title in Casablanca back in April and lost to Juan Carlos Ferrero in the Stuttgart final in July.